ABSTRACT
HIV-1 from infected subjects has been characterized in order to provide a more accurate view of the strains that are currently found in a given region. In this report, we focused on characterizing the pol gene diversity obtained from newly diagnosed patients in Santos metropolitan area, Brazil. This region is composed of nine cities and an international port. Analysis of the 33 samples revealed that 22 strains belonged to subtype B, 4 to subtype F, and 2 to subtype C; 5 strains were B/F recombinants. Our results demonstrated that 18.2% of samples were primary antiretroviral resistance genotypic mutations, with high-level resistance to reverse transcriptase inhibitors in both subtypes B and F and in recombinant forms B/F. Our data revealed that the primary antiretroviral resistance genotypic mutations should be carefully investigated in developing countries with widespread access to antiretrovirals, such as Brazil.
Subject(s)
Drug Resistance, Viral , Genetic Variation , HIV Infections/virology , HIV-1/classification , HIV-1/genetics , Adult , Anti-HIV Agents/pharmacology , Brazil , Cluster Analysis , Female , Genotype , HIV-1/isolation & purification , Humans , Male , Molecular Sequence Data , Mutation, Missense , Polymerase Chain Reaction , Recombination, Genetic , Reverse Transcriptase Inhibitors/pharmacology , Sequence Analysis, DNA , Sequence Homology , Urban Population , pol Gene Products, Human Immunodeficiency Virus/geneticsSubject(s)
Anti-HIV Agents , HIV-1/drug effects , RNA, Viral/drug effects , Reverse Transcriptase Inhibitors , Viremia , Adult , Anti-HIV Agents/pharmacology , Anti-HIV Agents/therapeutic use , Antiretroviral Therapy, Highly Active , Brazil/epidemiology , CD4 Lymphocyte Count , Drug Therapy, Combination , Female , HIV Infections/drug therapy , HIV Infections/epidemiology , HIV Infections/immunology , HIV Infections/virology , HIV-1/genetics , HIV-1/physiology , Humans , Male , National Health Programs , RNA, Viral/blood , Reverse Transcriptase Inhibitors/pharmacology , Reverse Transcriptase Inhibitors/therapeutic use , Time Factors , Treatment Outcome , Viral Load , Viremia/drug therapy , Viremia/epidemiology , Viremia/immunology , Viremia/virologyABSTRACT
HIV-1 antiretroviral drug resistance mutations in subtype B, F, and recombinants B/F in Santos, Brazil were characterized. We studied 83 samples from individuals enrolled at the Brazilian HIV/AIDS programs from Santos. These patients have been treated with multiantiretroviral therapy. Samples were collected in 2006; RNA was extracted from plasma and used as a target to amplify the pol gene of HIV-1. PCR products were sequenced on both strands, phylogenetic analyses were performed by neighbor-joining, and recombination was evaluated by bootscan. pol gene sequencing of the samples revealed that 54 strains belonged to subtype B, 4 were subtype F, 1 was subtype C, and 24 were B/F recombinants. Recombinant break points in 20 samples are the same identified in CRF28_BF and CRF29_BF. Drug resistance mutations identified in common to subtypes B, F, and recombinants B/F were protease inhibitors M46I/L (29%), I54V (24%), A71V (22%), and V82A/F (31%); reverse transcriptase nucleoside resistance mutations M41L (52%), D67N (30%), K70R (26%), M184V (88%), L210W (29%), T215Y/I/F (65%), and K219Q/E/N (28%); and reverse transcriptase nonnucleoside resistance mutation K103N (52%). Our results suggest that, in general, the same amino acids are emerging in both subtypes B, F, and recombinant forms BF due to the selective pressure of antiretrovirals. Recombinant break points in samples are the same as identified in CRF28_BF and CRF29_BF and are recognized as important for the evolution of the local epidemic.
Subject(s)
Drug Resistance, Viral/genetics , HIV Infections/virology , HIV-1/drug effects , HIV-1/genetics , Mutation , Polymorphism, Genetic , pol Gene Products, Human Immunodeficiency Virus/genetics , Adult , Amino Acid Sequence , Amino Acid Substitution/genetics , Anti-HIV Agents/pharmacology , Brazil , Cluster Analysis , Female , Genotype , HIV Protease/genetics , HIV Reverse Transcriptase/genetics , HIV-1/isolation & purification , Humans , Male , Molecular Sequence Data , Phylogeny , RNA, Viral/blood , RNA, Viral/genetics , RNA, Viral/isolation & purification , Recombination, Genetic , Reverse Transcriptase Polymerase Chain Reaction , Selection, Genetic , Sequence Alignment , Sequence Analysis, DNA , pol Gene Products, Human Immunodeficiency Virus/chemistryABSTRACT
The most prevalent HIV-1 clade in the global epidemics is C, and this clade is also becoming important in the Brazilian epidemics. In this study, we characterized HIV-1 subtype C variants by sequencing their near full-length genomes. DNA was extracted from six samples previously classified in our laboratory as subtype C on the basis of partial genome sequencing. Amplification was carried out by overlapping PCR followed by direct sequencing. Phylogenetic analysis of full length genomes confirmed that all isolates belonged to subtype C, which formed a highly supported monophyletic cluster and showed a nucleotide distance of 5.4%. The core promoter of all isolates contained three NF-kappaB binding motifs. Our results suggest that subtype C viruses circulating in Brazil were likely introduced recently from a unique point source. The independent clustering of Brazilian subtype C on the phylogenetic tree suggests the profile of an ideal local candidate for the development of a single subtype vaccine.
Subject(s)
Genome, Viral , HIV Infections/virology , HIV-1/genetics , Brazil , Genes, env , Genes, gag , Humans , Molecular Sequence Data , PhylogenyABSTRACT
Recombination is an important way to generate genetic diversity. Accumulation of HIV-1 full-length genomes in databases demonstrated that recombination is pervasive in viral strains collected globally. Recombinant forms achieving epidemiological relevance are termed circulating recombinant forms (CRFs). CRF12_BF was up to now the only CRF described in South America. The objective was to identify the first CRF in Brazil conducting full genome analysis of samples sharing the same partial genome recombinant structure. Ten samples obtained from individuals residing in Santos, Brazil, sharing the same recombination pattern based on partial genome sequence data, were selected from a larger group to undergo full length genome analysis. Near full length genomes were assembled from overlapping fragments. Mosaic genomes were evaluated by Bootscan, alignment inspection, and phylogenetic analysis using neighbor joining and maximum likelihood. Full genomes were also analyzed by split decomposition. We were able to identify five mosaic genomes. Two of these structures were represented by at least three samples derived from epidemiologically unlinked individuals. These structures were named CRF28_BF and CRF29_BF and are the second and third CRFs composed exclusively by subtypes B and F as well as the second and third CRFs encountered in South America. Other recombinant forms studied here resembled CRF28_BF and CRF29_BF. Our results suggest that a diverse population of related recombinants, including CRFs may play an important part in the Brazilian and South American epidemic.
